[English] 日本語
Yorodumi- PDB-5ubg: Catalytic core domain of Adenosine triphosphate phosphoribosyltra... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ubg | ||||||
---|---|---|---|---|---|---|---|
Title | Catalytic core domain of Adenosine triphosphate phosphoribosyltransferase from Campylobacter jejuni with bound Phosphoribosyl-ATP | ||||||
Components | ATP phosphoribosyltransferase | ||||||
Keywords | TRANSFERASE / Histidine-biosynthesis / HisG / PR-ATP | ||||||
Function / homology | Function and homology information ATP phosphoribosyltransferase / ATP phosphoribosyltransferase activity / L-histidine biosynthetic process / magnesium ion binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Campylobacter jejuni (Campylobacter) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Mittelstaedt, G. / Jiao, W. / Livingstone, E.K. / Parker, E.J. | ||||||
Citation | Journal: Biochem. J. / Year: 2018 Title: A dimeric catalytic core relates the short and long forms of ATP-phosphoribosyltransferase. Authors: Mittelstadt, G. / Jiao, W. / Livingstone, E.K. / Moggre, G.J. / Nazmi, A.R. / Parker, E.J. #1: Journal: Protein Sci. / Year: 2016 Title: Campylobacter jejuni adenosine triphosphate phosphoribosyltransferase is an active hexamer that is allosterically controlled by the twisting of a regulatory tail. Authors: Mittelstaedt, G. / Moggre, G.J. / Panjikar, S. / Nazmi, A.R. / Parker, E.J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5ubg.cif.gz | 202.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5ubg.ent.gz | 159.6 KB | Display | PDB format |
PDBx/mmJSON format | 5ubg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ub/5ubg ftp://data.pdbj.org/pub/pdb/validation_reports/ub/5ubg | HTTPS FTP |
---|
-Related structure data
Related structure data | 5ub9SC 5ubhC 5ubiC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||
Unit cell |
| ||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 0 / Auth seq-ID: 4 - 225 / Label seq-ID: 5 - 226
| ||||||||||||||||||
Details | The authors state that the protein exists as dimer with a molecular mass of 50 kDa in solution as evidenced by SEC, AUC, and light scattering experiments |
-Components
#1: Protein | Mass: 25340.268 Da / Num. of mol.: 2 / Fragment: residues 1-225 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Campylobacter jejuni (strain RM1221) (Campylobacter) Strain: RM1221 / Gene: hisG, CJE1769 / Plasmid: pDEST15 / Details (production host): N-terminal GST tag / Production host: Escherichia coli (E. coli) / Strain (production host): BL21*(DE3) / References: UniProt: Q5HSJ4, ATP phosphoribosyltransferase #2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 50.46 % / Description: octahedral shape |
---|---|
Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 0.1 M sodium acetate pH 5.0, 0.01 M ZnCl2, 7-10% PEG 6000, formed crystals soaked with 5 mM PR-ATP for 30-60 min PH range: 5 / Temp details: temperature controlled |
-Data collection
Diffraction | Mean temperature: 80 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.959 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 2, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.959 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→34.55 Å / Num. obs: 40502 / % possible obs: 99.8 % / Redundancy: 10.8 % / CC1/2: 1 / Rmerge(I) obs: 0.067 / Net I/σ(I): 23.9 |
Reflection shell | Resolution: 1.9→1.94 Å / Redundancy: 10.5 % / Rmerge(I) obs: 0.91 / Mean I/σ(I) obs: 3.2 / CC1/2: 0.769 / % possible all: 97.1 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: single chain of PDB 5UB9 Resolution: 1.9→34.55 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.948 / SU B: 5.913 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.029 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.602 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.9→34.55 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|